Edge Marking not rendering
I think your problem is in Freestyle's logic of inclusion and exclusion.

In any one Line Set, the relation between 'Select By' Methods is logical AND.

Here's an example cube with extrusions:



The inner cube's edges are marked Freestyle. The extrusions' outer faces are marked Freestyle.

If you 'Select By' Edge Type, (Inclusive, OR, Marked Edges) you get this:



If you 'Select By' Face Mark (Inclusive, One Face) you get this:



So far, so good.. but if you combine both 'Select By' criteria in the same Line Set, you get this:



.. because there are no edges that satisfy both criteria.

So the rule of thumb, to keep life simple, unless you need to make peculiar selections, is to restrict yourself to one 'Select By' method plus 'Visibility' per Line Set. If you need to select by two different methods, it will usually be a good idea to put them in different Line Sets: